README+s.md

ARGweavers

Pre-requisites

1. rustup
2. CMake with any modern C++ compiler
3. rye or maturin for Python binding
4. samtools for smc2bed-all

Install

foo@bar:~$ pip install argweaver+git://github.com/tcztzy/argweavers

After install the Python package, you don't need any additional steps to use the binaries, all the binaries are installed to the Python environment's bin directory.

This repository provides Python wrappers for the following programs:

• arg-likelihood
• arg-sample
• arg-summarize

And rewrite of the following programs:

• smc2bed and rust version
• smc2bed-all

Usage

foo@bar:~$ smc2bed-all --help
usage: smc2bed-all [-h] [-s <startnum>] [-e <endnum>] [-i <interval>]
                   [-r <region>]
                   <baseout>

Convert all *.smc files from a single arg-sample run into a bed.gz file
which can be parsed by arg-summarize

positional arguments:
  <baseout>      base name of arg-sample output (specified with arg-sample
                 -o). Creates a file called <baseout>.bed.gz.

optional arguments:
  -h, --help     show this help message and exit
  -s <startnum>  start with this MCMC rep of arg-sample (default: 0)
  -e <endnum>    end with this MCMC rep (default: stop when no file exists)
  -i <interval>  sampling interval (will be auto-detected from output if not
                 specified)
  -r <region>    region (in format START-END, 1-based, inclusive) to pass to
                 smc2bed (default: run on all coordinates)

Build

foo@bar:~$ git clone https://github.com/tcztzy/argweaver
foo@bar:~$ cd argweaver
foo@bar:~/argweaver$ cargo build --release

Develop

foo@bar:~/argweaver$ rye sync # Or `maturin dev`
foo@bar:~/argweaver$ pre-commit install

Test

foo@bar:~/argweaver$ cargo test                # test the Rust library
foo@bar:~/argweaver$ rye sync --features test  # install pytest
foo@bar:~/argweaver$ pytest                    # test the Python binding